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authorKen Kellner <ken@kenkellner.com>2018-08-31 15:33:52 (GMT)
committerKen Kellner <ken@kenkellner.com>2018-08-31 15:33:52 (GMT)
commitbe1d58e52458fbbadaefc72f6dd1b02264ff7f76 (patch)
treeefa315722d565c95c07817061753378c5fbda3bb
parent1904e1fa971f0d23a4a895f7c355bb8428e0e76b (diff)
Updates to talk for Clemson 2018
-rw-r--r--.gitignore2
-rw-r--r--common.tex9
-rw-r--r--content.md12
-rw-r--r--ecology.bst1460
-rw-r--r--figures.R103
-rw-r--r--hee_map.R85
-rw-r--r--makefile21
-rw-r--r--talk.tex5
8 files changed, 128 insertions, 1569 deletions
diff --git a/.gitignore b/.gitignore
index 7ad78e5..5f821b3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,8 @@
*.blg
*.bst
*.bib
+*.bcf
+*.run.xml
content.tex
datasources.R
images/*
diff --git a/common.tex b/common.tex
index d9779bc..1922f1c 100644
--- a/common.tex
+++ b/common.tex
@@ -1,5 +1,5 @@
\title{Wildlife in managed forests: \\ demographic patterns and trophic interactions}
-\date{31 January 2018}
+\date{20 September 2018}
\author{\textbf{Ken Kellner}}
%\institute{Forestry and Natural Resources, Purdue University}
%\setbeamertemplate{frame footer}{Kellner - Demo Talk}
@@ -11,9 +11,10 @@
\definecolor{firebrick}{HTML}{FF3030}
\definecolor{brickred}{HTML}{CB4154}
-\usepackage[comma,sort]{natbib}
-\bibliographystyle{style}
-\renewcommand{\bibsection}{}
+\usepackage[doi=false,isbn=false,url=false,backend=biber,
+ style=chicago-authordate]{biblatex}
+\addbibresource{references.bib}
+\AtEveryBibitem{\clearfield{addendum}}
\lstset{
language=R, % the language of the code
diff --git a/content.md b/content.md
index d6b5980..9677998 100644
--- a/content.md
+++ b/content.md
@@ -149,7 +149,7 @@ How does timber harvesting affect:
\column{.5\textwidth}
\centering
-\includegraphics[height=2.5in]{hee_area_transparent.pdf}
+\includegraphics[height=2.5in]{hee_map.pdf}
\colend
## Before-After Control-Impact Design
@@ -186,9 +186,13 @@ How does timber harvesting affect:
**How does harvest affect the bird community?**
## Breeding Bird Sampling
-
+\colbegin
+\column{.4\paperwidth}
\centering
-\includegraphics[height=2.7in]{hee_cores_transparent.pdf}
+\includegraphics[height=2.7in]{hee_map_sub.pdf}
+\column{.5\paperwidth}
+\includegraphics[height=2.7in]{hee_cores.pdf}
+\colend
## Bird Response Summary
\ftline{\cite{Kellner2016d}}
@@ -378,5 +382,5 @@ Does this affect oak regeneration success?
## Questions
\LARGE
-kenneth.kellner@mail.wvu.edu
+ken@kenkellner.com
diff --git a/ecology.bst b/ecology.bst
deleted file mode 100644
index e6cd0ee..0000000
--- a/ecology.bst
+++ /dev/null
@@ -1,1460 +0,0 @@
- % *** LaTeX Bibliography style for Ecology ***
- % Version 1.2.1, 23/November/2004
- % Copyright 2004 Henrique M. Pereira (hpereira@stanfordalumni.org)
- %
- %
- % This file formats a bibliography as used by the Ecology journal,
- % published by the Ecological Society of America. I used makebst
- % and merlin.mbs from Patrick W. Daly (see below) to produce a
- % first version which was then modified to conform closer to Ecology.
- % This file has to be used in conjunction with the natbib.sty package.
- %
- % Include immediately before \begin{document} the natbib command
- % \bibpunct{(}{)}{,}{a}{}{;} so that no commas are used in citations
- % between author and year.
- %
- % Version History:
- % 1.2 Added comma in the middle of a citation with two authors
- % 1.1 Several modifications to make it conform closer to Ecology
- % 1.0 Basic functionality
- %
- % DISCLAIMER: No warranties of any kind are given that this will produce
- % the exact bibliographic format for Ecology.
- %=================================================================
- %
- % The original source file was:
- % merlin.mbs (with options: `ay,nat,nm-rev1,jnrlst,xlab-it,keyxyr,dt-beg,note-yr,jttl-rm,vol-bf,vnum-x,num-xser,numser,jnm-x,btit-rm,bt-rm,xedn,url,url-blk')
- % Name and version information of the main mbs file:
- % \ProvidesFile{merlin.mbs}[2002/01/14 4.03 (PWD, AO, DPC)]
- % For use with BibTeX version 0.99a or later
- % ----------------------------------------
- %
- % Copyright 1994-2002 Patrick W Daly
- %
- % IMPORTANT NOTICE:
- % This bibliographic style (bst) file has been generated from one or
- % more master bibliographic style (mbs) files, listed above.
- %
- % This generated file can be redistributed and/or modified under the terms
- % of the LaTeX Project Public License Distributed from CTAN
- % archives in directory macros/latex/base/lppl.txt; either
- % version 1 of the License, or any later version.
- %
- %===============================================================
- %
- % This bibliography style file is intended for texts in ENGLISH
- % This is an author-year citation style bibliography. As such, it is
- % non-standard LaTeX, and requires a special package file to function properly.
- % Such a package is natbib.sty by Patrick W. Daly
- % The form of the \bibitem entries is
- % \bibitem[Jones et al.(1990)]{key}...
- % \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}...
- % The essential feature is that the label (the part in brackets) consists
- % of the author names, as they should appear in the citation, with the year
- % in parentheses following. There must be no space before the opening
- % parenthesis!
- % With natbib v5.3, a full list of authors may also follow the year.
- % In natbib.sty, it is possible to define the type of enclosures that is
- % really wanted (brackets or parentheses), but in either case, there must
- % be parentheses in the label.
- % The \cite command functions as follows:
- % \citet{key} ==>> Jones et al. (1990)
- % \citet*{key} ==>> Jones, Baker, and Smith (1990)
- % \citep{key} ==>> (Jones et al., 1990)
- % \citep*{key} ==>> (Jones, Baker, and Smith, 1990)
- % \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2)
- % \citep[e.g.][]{key} ==>> (e.g. Jones et al., 1990)
- % \citep[e.g.][p. 32]{key} ==>> (e.g. Jones et al., p. 32)
- % \citeauthor{key} ==>> Jones et al.
- % \citeauthor*{key} ==>> Jones, Baker, and Smith
- % \citeyear{key} ==>> 1990
- %---------------------------------------------------------------------
-
-ENTRY
- { address
- author
- booktitle
- chapter
- edition
- editor
- howpublished
- institution
- journal
- key
- month
- note
- number
- organization
- pages
- publisher
- school
- series
- title
- type
- url
- volume
- year
- }
- {}
- { label extra.label sort.label short.list }
-INTEGERS { output.state before.all mid.sentence after.sentence after.block }
-FUNCTION {init.state.consts}
-{ #0 'before.all :=
- #1 'mid.sentence :=
- #2 'after.sentence :=
- #3 'after.block :=
-}
-STRINGS { s t}
-FUNCTION {output.nonnull}
-{ 's :=
- output.state mid.sentence =
- { ", " * write$ }
- { output.state after.block =
- { add.period$ write$
- newline$
- "\newblock " write$
- }
- { output.state before.all =
- 'write$
- { add.period$ " " * write$ }
- if$
- }
- if$
- mid.sentence 'output.state :=
- }
- if$
- s
-}
-FUNCTION {output}
-{ duplicate$ empty$
- 'pop$
- 'output.nonnull
- if$
-}
-FUNCTION {output.check}
-{ 't :=
- duplicate$ empty$
- { pop$ "empty " t * " in " * cite$ * warning$ }
- 'output.nonnull
- if$
-}
-FUNCTION {fin.entry}
-{ add.period$
- write$
- newline$
-}
-
-FUNCTION {new.block}
-{ output.state before.all =
- 'skip$
- { after.block 'output.state := }
- if$
-}
-FUNCTION {new.sentence}
-{ output.state after.block =
- 'skip$
- { output.state before.all =
- 'skip$
- { after.sentence 'output.state := }
- if$
- }
- if$
-}
-FUNCTION {add.blank}
-{ " " * before.all 'output.state :=
-}
-
-FUNCTION {date.block}
-{
- new.block
-}
-
-FUNCTION {not}
-{ { #0 }
- { #1 }
- if$
-}
-FUNCTION {and}
-{ 'skip$
- { pop$ #0 }
- if$
-}
-FUNCTION {or}
-{ { pop$ #1 }
- 'skip$
- if$
-}
-FUNCTION {new.block.checkb}
-{ empty$
- swap$ empty$
- and
- 'skip$
- 'new.block
- if$
-}
-FUNCTION {field.or.null}
-{ duplicate$ empty$
- { pop$ "" }
- 'skip$
- if$
-}
-FUNCTION {emphasize}
-{ duplicate$ empty$
- { pop$ "" }
- { "{\em " swap$ * "\/}" * }
- if$
-}
-FUNCTION {bolden}
-{ duplicate$ empty$
- { pop$ "" }
- { "{\bf " swap$ * "}" * }
- if$
-}
-FUNCTION {tie.or.space.prefix}
-{ duplicate$ text.length$ #3 <
- { "~" }
- { " " }
- if$
- swap$
-}
-
-FUNCTION {capitalize}
-{ "u" change.case$ "t" change.case$ }
-
-FUNCTION {space.word}
-{ " " swap$ * " " * }
- % Here are the language-specific definitions for explicit words.
- % Each function has a name bbl.xxx where xxx is the English word.
- % The language selected here is ENGLISH
-FUNCTION {bbl.and}
-{ "and"}
-
-FUNCTION {bbl.etal}
-{ "et~al." }
-
-FUNCTION {bbl.editors}
-{ "editors" }
-
-FUNCTION {bbl.editor}
-{ "editor" }
-
-FUNCTION {bbl.edby}
-{ "edited by" }
-
-FUNCTION {bbl.edition}
-{ "edition" }
-
-FUNCTION {bbl.volume}
-{ "volume" }
-
-FUNCTION {bbl.of}
-{ "of" }
-
-FUNCTION {bbl.number}
-{ "number" }
-
-FUNCTION {bbl.nr}
-{ "no." }
-
-FUNCTION {bbl.in}
-{ "in" }
-
-FUNCTION {bbl.pages}
-{ "pages" }
-
-FUNCTION {bbl.page}
-{ "page" }
-
-FUNCTION {bbl.chapter}
-{ "chapter" }
-
-FUNCTION {bbl.techrep}
-{ "Technical Report" }
-
-FUNCTION {bbl.mthesis}
-{ "Master's thesis" }
-
-FUNCTION {bbl.phdthesis}
-{ "Ph.D. thesis" }
-
-MACRO {jan} {"January"}
-
-MACRO {feb} {"February"}
-
-MACRO {mar} {"March"}
-
-MACRO {apr} {"April"}
-
-MACRO {may} {"May"}
-
-MACRO {jun} {"June"}
-
-MACRO {jul} {"July"}
-
-MACRO {aug} {"August"}
-
-MACRO {sep} {"September"}
-
-MACRO {oct} {"October"}
-
-MACRO {nov} {"November"}
-
-MACRO {dec} {"December"}
-
-
-FUNCTION {bibinfo.check}
-{ swap$
- duplicate$ missing$
- {
- pop$ pop$
- ""
- }
- { duplicate$ empty$
- {
- swap$ pop$
- }
- { swap$
- pop$
- }
- if$
- }
- if$
-}
-FUNCTION {bibinfo.warn}
-{ swap$
- duplicate$ missing$
- {
- swap$ "missing " swap$ * " in " * cite$ * warning$ pop$
- ""
- }
- { duplicate$ empty$
- {
- swap$ "empty " swap$ * " in " * cite$ * warning$
- }
- { swap$
- pop$
- }
- if$
- }
- if$
-}
-FUNCTION {format.url}
-{ url empty$
- { "" }
- { "\urlprefix\url{" url * "}" * }
- if$
-}
-
-STRINGS { bibinfo}
-INTEGERS { nameptr namesleft numnames }
-
-FUNCTION {format.names}
-{ 'bibinfo :=
- duplicate$ empty$ 'skip$ {
- 's :=
- "" 't :=
- #1 'nameptr :=
- s num.names$ 'numnames :=
- numnames 'namesleft :=
- { namesleft #0 > }
- { s nameptr
- duplicate$ #1 >
- { "{f.~}{vv~}{ll}{, jj}" }
- { "{vv~}{ll}{, f.}{, jj}" }
- if$
- format.name$
- bibinfo bibinfo.check
- 't :=
- nameptr #1 >
- {
- namesleft #1 >
- { ", " * t * }
- {
- %Changed from 2 to 1 to add comma in the middle of two names
- numnames #1 >
- { "," * }
- 'skip$
- if$
- s nameptr "{ll}" format.name$ duplicate$ "others" =
- { 't := }
- { pop$ }
- if$
- t "others" =
- {
- " " * bbl.etal *
- }
- {
- bbl.and
- space.word * t *
- }
- if$
- }
- if$
- }
- 't
- if$
- nameptr #1 + 'nameptr :=
- namesleft #1 - 'namesleft :=
- }
- while$
- } if$
-}
-FUNCTION {format.names.ed}
-{
- 'bibinfo :=
- duplicate$ empty$ 'skip$ {
- 's :=
- "" 't :=
- #1 'nameptr :=
- s num.names$ 'numnames :=
- numnames 'namesleft :=
- { namesleft #0 > }
- { s nameptr
- "{f.~}{vv~}{ll}{, jj}"
- format.name$
- bibinfo bibinfo.check
- 't :=
- nameptr #1 >
- {
- namesleft #1 >
- { ", " * t * }
- {
- numnames #2 >
- { "," * }
- 'skip$
- if$
- s nameptr "{ll}" format.name$ duplicate$ "others" =
- { 't := }
- { pop$ }
- if$
- t "others" =
- {
-
- " " * bbl.etal *
- }
- {
- bbl.and
- space.word * t *
- }
- if$
- }
- if$
- }
- 't
- if$
- nameptr #1 + 'nameptr :=
- namesleft #1 - 'namesleft :=
- }
- while$
- } if$
-}
-FUNCTION {format.key}
-{ empty$
- { key field.or.null }
- { "" }
- if$
-}
-
-FUNCTION {format.authors}
-{ author "author" format.names
-}
-FUNCTION {get.bbl.editor}
-{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ }
-
-FUNCTION {format.editors}
-{ editor "editor" format.names duplicate$ empty$ 'skip$
- {
- "," *
- " " *
- get.bbl.editor
- *
- }
- if$
-}
-FUNCTION {format.note}
-{
- note empty$
- { "" }
- { note #1 #1 substring$
- duplicate$ "{" =
- 'skip$
- { output.state mid.sentence =
- { "l" }
- { "u" }
- if$
- change.case$
- }
- if$
- note #2 global.max$ substring$ * "note" bibinfo.check
- }
- if$
-}
-
-FUNCTION {format.title}
-{ title
- % changing case
- %duplicate$ empty$ 'skip$
- % { "t" change.case$ }
- %if$
- "title" bibinfo.check
-}
-FUNCTION {format.full.names}
-{'s :=
- "" 't :=
- #1 'nameptr :=
- s num.names$ 'numnames :=
- numnames 'namesleft :=
- { namesleft #0 > }
- { s nameptr
- "{vv~}{ll}" format.name$
- 't :=
- nameptr #1 >
- {
- namesleft #1 >
- { ", " * t * }
- {
- s nameptr "{ll}" format.name$ duplicate$ "others" =
- { 't := }
- { pop$ }
- if$
- t "others" =
- {
- " " * bbl.etal *
- }
- {
- numnames #2 >
- { "," * }
- 'skip$
- if$
- bbl.and
- space.word * t *
- }
- if$
- }
- if$
- }
- 't
- if$
- nameptr #1 + 'nameptr :=
- namesleft #1 - 'namesleft :=
- }
- while$
-}
-
-FUNCTION {author.editor.key.full}
-{ author empty$
- { editor empty$
- { key empty$
- { cite$ #1 #3 substring$ }
- 'key
- if$
- }
- { editor format.full.names }
- if$
- }
- { author format.full.names }
- if$
-}
-
-FUNCTION {author.key.full}
-{ author empty$
- { key empty$
- { cite$ #1 #3 substring$ }
- 'key
- if$
- }
- { author format.full.names }
- if$
-}
-
-FUNCTION {editor.key.full}
-{ editor empty$
- { key empty$
- { cite$ #1 #3 substring$ }
- 'key
- if$
- }
- { editor format.full.names }
- if$
-}
-
-FUNCTION {make.full.names}
-{ type$ "book" =
- type$ "inbook" =
- or
- 'author.editor.key.full
- { type$ "proceedings" =
- 'editor.key.full
- 'author.key.full
- if$
- }
- if$
-}
-
-FUNCTION {output.bibitem}
-{ newline$
- "\bibitem[{" write$
- label write$
- ")" make.full.names duplicate$ short.list =
- { pop$ }
- { * }
- if$
- "}]{" * write$
- cite$ write$
- "}" write$
- newline$
- ""
- before.all 'output.state :=
-}
-
-FUNCTION {n.dashify}
-{
- 't :=
- ""
- { t empty$ not }
- { t #1 #1 substring$ "-" =
- { t #1 #2 substring$ "--" = not
- { "--" *
- t #2 global.max$ substring$ 't :=
- }
- { { t #1 #1 substring$ "-" = }
- { "-" *
- t #2 global.max$ substring$ 't :=
- }
- while$
- }
- if$
- }
- { t #1 #1 substring$ *
- t #2 global.max$ substring$ 't :=
- }
- if$
- }
- while$
-}
-
-FUNCTION {word.in}
-{ bbl.in capitalize
- " " * }
-
-FUNCTION {format.date}
-{ year "year" bibinfo.check duplicate$ empty$
- {
- "empty year in " cite$ * "; set to ????" * warning$
- pop$ "????"
- }
- 'skip$
- if$
- extra.label *
-}
-FUNCTION {format.btitle}
-{ title "title" bibinfo.check
- duplicate$ empty$ 'skip$
- {
- }
- if$
-}
-FUNCTION {either.or.check}
-{ empty$
- 'pop$
- { "can't use both " swap$ * " fields in " * cite$ * warning$ }
- if$
-}
-FUNCTION {format.bvolume}
-{ volume empty$
- { "" }
- { bbl.volume volume tie.or.space.prefix
- "volume" bibinfo.check * *
- series "series" bibinfo.check
- duplicate$ empty$ 'pop$
- { swap$ bbl.of space.word * swap$
- emphasize * }
- if$
- "volume and number" number either.or.check
- }
- if$
-}
-FUNCTION {format.number.series}
-{ volume empty$
- { number empty$
- { series field.or.null }
- { series empty$
- { number "number" bibinfo.check }
- { output.state mid.sentence =
- { bbl.number }
- { bbl.number capitalize }
- if$
- number tie.or.space.prefix "number" bibinfo.check * *
- bbl.in space.word *
- series "series" bibinfo.check *
- }
- if$
- }
- if$
- }
- { "" }
- if$
-}
-
-FUNCTION {format.edition}
-{ edition duplicate$ empty$ 'skip$
- {
- output.state mid.sentence =
- { "l" }
- { "t" }
- if$ change.case$
- "edition" bibinfo.check
- " " * bbl.edition *
- }
- if$
-}
-INTEGERS { multiresult }
-FUNCTION {multi.page.check}
-{ 't :=
- #0 'multiresult :=
- { multiresult not
- t empty$ not
- and
- }
- { t #1 #1 substring$
- duplicate$ "-" =
- swap$ duplicate$ "," =
- swap$ "+" =
- or or
- { #1 'multiresult := }
- { t #2 global.max$ substring$ 't := }
- if$
- }
- while$
- multiresult
-}
-FUNCTION {format.pages}
-{ pages duplicate$ empty$ 'skip$
- { duplicate$ multi.page.check
- {
- bbl.pages swap$
- n.dashify
- }
- {
- bbl.page swap$
- }
- if$
- tie.or.space.prefix
- "pages" bibinfo.check
- * *
- }
- if$
-}
-FUNCTION {format.journal.pages}
-{ pages duplicate$ empty$ 'pop$
- { swap$ duplicate$ empty$
- { pop$ pop$ format.pages }
- {
- ":" *
- swap$
- n.dashify
- "pages" bibinfo.check
- *
- }
- if$
- }
- if$
-}
-FUNCTION {format.vol.num.pages}
-{ volume field.or.null
- duplicate$ empty$ 'skip$
- {
- "volume" bibinfo.check
- }
- if$
- bolden
- format.journal.pages
-}
-
-FUNCTION {format.chapter.pages}
-{ chapter empty$
- 'format.pages
- { type empty$
- { bbl.chapter }
- { type "l" change.case$
- "type" bibinfo.check
- }
- if$
- chapter tie.or.space.prefix
- "chapter" bibinfo.check
- * *
- pages empty$
- 'skip$
- { ", " * format.pages * }
- if$
- }
- if$
- capitalize
- " " * %appends a space before "in"
-}
-
-FUNCTION {format.booktitle}
-{
- booktitle "booktitle" bibinfo.check
-}
-FUNCTION {format.in.ed.booktitle}
-{ format.booktitle duplicate$ empty$ 'skip$
- {
- editor "editor" format.names.ed duplicate$ empty$ 'pop$
- {
- "," *
- " " *
- get.bbl.editor
- ". " *
- * swap$
- * }
- if$
- bbl.in emphasize " " *
- swap$ *
- }
- if$
-}
-FUNCTION {format.thesis.type}
-{ type duplicate$ empty$
- 'pop$
- { swap$ pop$
- "t" change.case$ "type" bibinfo.check
- }
- if$
-}
-FUNCTION {format.tr.number}
-{ number "number" bibinfo.check
- type duplicate$ empty$
- { pop$ bbl.techrep }
- 'skip$
- if$
- "type" bibinfo.check
- swap$ duplicate$ empty$
- { pop$ "t" change.case$ }
- { tie.or.space.prefix * * }
- if$
-}
-FUNCTION {format.article.crossref}
-{
- word.in
- " \cite{" * crossref * "}" *
-}
-FUNCTION {format.book.crossref}
-{ volume duplicate$ empty$
- { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
- pop$ word.in
- }
- { bbl.volume
- capitalize
- swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word *
- }
- if$
- " \cite{" * crossref * "}" *
-}
-FUNCTION {format.incoll.inproc.crossref}
-{
- word.in
- " \cite{" * crossref * "}" *
-}
-FUNCTION {format.org.or.pub}
-{ 't :=
- ""
- address empty$ t empty$ and
- 'skip$
- {
- t empty$
- { address "address" bibinfo.check *
- }
- { t *
- address empty$
- 'skip$
- { ", " * address "address" bibinfo.check * }
- if$
- }
- if$
- }
- if$
-}
-FUNCTION {format.publisher.address}
-{ publisher "publisher" bibinfo.warn format.org.or.pub
-}
-
-FUNCTION {format.organization.address}
-{ organization "organization" bibinfo.check format.org.or.pub
-}
-
-FUNCTION {article}
-{ output.bibitem
- format.authors "author" output.check
- author format.key output
- new.block %added to put dot at end of authors
- format.date "year" output.check
- date.block
- format.title "title" output.check
- new.block
- crossref missing$
- {
- journal
- "journal" bibinfo.check
- "journal" output.check
- add.blank
- format.vol.num.pages output
- }
- { format.article.crossref output.nonnull
- format.pages output
- }
- if$
- new.block
- format.url output
- fin.entry
-}
-FUNCTION {book}
-{ output.bibitem
- author empty$
- { format.editors "author and editor" output.check
- editor format.key output
- }
- { format.authors output.nonnull
- crossref missing$
- { "author and editor" editor either.or.check }
- 'skip$
- if$
- }
- if$
- new.block %added to put dot at end of authors
- format.date "year" output.check
- date.block
- format.btitle "title" output.check
- crossref missing$
- { %format.bvolume output removed to not include series in references
- new.block
- new.sentence
- format.edition output
- new.block
- format.number.series output
- format.publisher.address output
- }
- {
- new.block
- format.book.crossref output.nonnull
- }
- if$
- new.block
- format.url output
- fin.entry
-}
-FUNCTION {booklet}
-{ output.bibitem
- format.authors output
- author format.key output
- format.date "year" output.check
- date.block
- format.title "title" output.check
- new.block
- howpublished "howpublished" bibinfo.check output
- address "address" bibinfo.check output
- new.block
- format.url output
- fin.entry
-}
-
-FUNCTION {inbook}
-{ output.bibitem
- author empty$
- { format.editors "author and editor" output.check
- editor format.key output
- }
- { format.authors output.nonnull
- crossref missing$
- { "author and editor" editor either.or.check }
- 'skip$
- if$
- }
- if$
- format.date "year" output.check
- date.block
- format.btitle "title" output.check
- crossref missing$
- {
- format.bvolume output
- format.chapter.pages "chapter and pages" output.check
- new.block
- new.sentence
- format.number.series output
- format.publisher.address output
- }
- {
- format.chapter.pages "chapter and pages" output.check
- new.block
- format.book.crossref output.nonnull
- }
- if$
- format.edition output
- new.block
- format.url output
- fin.entry
-}
-
-FUNCTION {incollection}
-{ output.bibitem
- format.authors "author" output.check
- author format.key output
- format.date "year" output.check
- date.block
- format.title "title" output.check
- new.block
- crossref missing$
- {
- format.chapter.pages format.in.ed.booktitle * %appends pages and tittle
- "booktitle" output.check
- format.bvolume output
- new.sentence
- format.number.series output
- format.publisher.address output
- format.edition output
- }
- { format.incoll.inproc.crossref output.nonnull
- format.chapter.pages output
- }
- if$
- new.block
- format.url output
- fin.entry
-}
-FUNCTION {inproceedings}
-{
- output.bibitem
- format.authors "author" output.check
- author format.key output
- format.date "year" output.check
- date.block
- format.title "title" output.check
- new.block
- crossref missing$
- { format.chapter.pages format.in.ed.booktitle * %appends pages and tittle
- "booktitle" output.check
- format.bvolume output
- new.sentence
- format.number.series output
- publisher empty$
- { format.organization.address output }
- { organization "organization" bibinfo.check output
- format.publisher.address output
- }
- if$
- }
- { format.incoll.inproc.crossref output.nonnull
- format.pages output
- }
- if$
- new.block
- format.url output
- fin.entry
-}
-FUNCTION {conference} { inproceedings }
-FUNCTION {manual}
-{ output.bibitem
- format.authors output
- author format.key output
- format.date "year" output.check
- date.block
- format.btitle "title" output.check
- organization address new.block.checkb
- organization "organization" bibinfo.check output
- address "address" bibinfo.check output
- format.edition output
- new.block
- format.url output
- fin.entry
-}
-
-FUNCTION {mastersthesis}
-{ output.bibitem
- format.authors "author" output.check
- author format.key output
- format.date "year" output.check
- date.block
- format.btitle
- "title" output.check
- new.block
- bbl.mthesis format.thesis.type output.nonnull
- school "school" bibinfo.warn output
- address "address" bibinfo.check output
- new.block
- format.url output
- fin.entry
-}
-
-FUNCTION {misc}
-{ output.bibitem
- format.authors output
- author format.key output
- format.date "year" output.check
- date.block
- format.title output
- new.block
- howpublished "howpublished" bibinfo.check output
- new.block
- format.url output
- fin.entry
-}
-FUNCTION {phdthesis}
-{ output.bibitem
- format.authors "author" output.check
- author format.key output
- format.date "year" output.check
- date.block
- format.btitle
- "title" output.check
- new.block
- bbl.phdthesis format.thesis.type output.nonnull
- school "school" bibinfo.warn output
- address "address" bibinfo.check output
- new.block
- format.url output
- fin.entry
-}
-
-FUNCTION {proceedings}
-{ output.bibitem
- format.editors output
- editor format.key output
- format.date "year" output.check
- date.block
- format.btitle "title" output.check
- format.bvolume output
- new.sentence
- format.number.series output
- publisher empty$
- { format.organization.address output }
- { organization "organization" bibinfo.check output
- format.publisher.address output
- }
- if$
- new.block
- format.url output
- fin.entry
-}
-
-FUNCTION {techreport}
-{ output.bibitem
- format.authors "author" output.check
- author format.key output
- format.date "year" output.check
- date.block
- format.title
- "title" output.check
- new.block
- format.tr.number output.nonnull
- institution "institution" bibinfo.warn output
- address "address" bibinfo.check output
- new.block
- format.url output
- fin.entry
-}
-
-FUNCTION {unpublished}
-{ output.bibitem
- format.authors "author" output.check
- author format.key output
- format.date "year" output.check
- date.block
- format.title "title" output.check
- new.block
- format.url output
- new.block
- format.note "note" output.check
- fin.entry
-}
-
-FUNCTION {default.type} { misc }
-READ
-FUNCTION {sortify}
-{ purify$
- "l" change.case$
-}
-INTEGERS { len }
-FUNCTION {chop.word}
-{ 's :=
- 'len :=
- s #1 len substring$ =
- { s len #1 + global.max$ substring$ }
- 's
- if$
-}
-FUNCTION {format.lab.names}
-{ 's :=
- "" 't :=
- s #1 "{vv~}{ll}" format.name$
- s num.names$ duplicate$
- #2 >
- { pop$
- " " * bbl.etal *
- }
- { #2 <
- 'skip$
- { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
- {
- " " * bbl.etal *
- }
- { bbl.and space.word * s #2 "{vv~}{ll}" format.name$
- * }
- if$
- }
- if$
- }
- if$
-}
-
-FUNCTION {author.key.label}
-{ author empty$
- { key empty$
- { cite$ #1 #3 substring$ }
- 'key
- if$
- }
- { author format.lab.names }
- if$
-}
-
-FUNCTION {author.editor.key.label}
-{ author empty$
- { editor empty$
- { key empty$
- { cite$ #1 #3 substring$ }
- 'key
- if$
- }
- { editor format.lab.names }
- if$
- }
- { author format.lab.names }
- if$
-}
-
-FUNCTION {editor.key.label}
-{ editor empty$
- { key empty$
- { cite$ #1 #3 substring$ }
- 'key
- if$
- }
- { editor format.lab.names }
- if$
-}
-
-FUNCTION {calc.short.authors}
-{ type$ "book" =
- type$ "inbook" =
- or
- 'author.editor.key.label
- { type$ "proceedings" =
- 'editor.key.label
- 'author.key.label
- if$
- }
- if$
- 'short.list :=
-}
-
-FUNCTION {calc.label}
-{ calc.short.authors
- short.list
- "("
- *
- year duplicate$ empty$
- short.list key field.or.null = or
- { pop$ "" }
- 'skip$
- if$
- *
- 'label :=
-}
-
-FUNCTION {sort.format.names}
-{ 's :=
- #1 'nameptr :=
- ""
- s num.names$ 'numnames :=
- numnames 'namesleft :=
- { namesleft #0 > }
- { s nameptr
- "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}"
- format.name$ 't :=
- nameptr #1 >
- {
- " " *
- namesleft #1 = t "others" = and
- { "zzzzz" * }
- { t sortify * }
- if$
- }
- { t sortify * }
- if$
- nameptr #1 + 'nameptr :=
- namesleft #1 - 'namesleft :=
- }
- while$
-}
-
-FUNCTION {sort.format.title}
-{ 't :=
- "A " #2
- "An " #3
- "The " #4 t chop.word
- chop.word
- chop.word
- sortify
- #1 global.max$ substring$
-}
-FUNCTION {author.sort}
-{ author empty$
- { key empty$
- { "to sort, need author or key in " cite$ * warning$
- ""
- }
- { key sortify }
- if$
- }
- { author sort.format.names }
- if$
-}
-FUNCTION {author.editor.sort}
-{ author empty$
- { editor empty$
- { key empty$
- { "to sort, need author, editor, or key in " cite$ * warning$
- ""
- }
- { key sortify }
- if$
- }
- { editor sort.format.names }
- if$
- }
- { author sort.format.names }
- if$
-}
-FUNCTION {editor.sort}
-{ editor empty$
- { key empty$
- { "to sort, need editor or key in " cite$ * warning$
- ""
- }
- { key sortify }
- if$
- }
- { editor sort.format.names }
- if$
-}
-FUNCTION {presort}
-{ calc.label
- label sortify
- " "
- *
- type$ "book" =
- type$ "inbook" =
- or
- 'author.editor.sort
- { type$ "proceedings" =
- 'editor.sort
- 'author.sort
- if$
- }
- if$
- #1 entry.max$ substring$
- 'sort.label :=
- sort.label
- *
- " "
- *
- title field.or.null
- sort.format.title
- *
- #1 entry.max$ substring$
- 'sort.key$ :=
-}
-
-ITERATE {presort}
-SORT
-STRINGS { last.label next.extra }
-INTEGERS { last.extra.num number.label }
-FUNCTION {initialize.extra.label.stuff}
-{ #0 int.to.chr$ 'last.label :=
- "" 'next.extra :=
- #0 'last.extra.num :=
- #0 'number.label :=
-}
-FUNCTION {forward.pass}
-{ last.label label =
- { last.extra.num #1 + 'last.extra.num :=
- last.extra.num int.to.chr$ 'extra.label :=
- }
- { "a" chr.to.int$ 'last.extra.num :=
- "" 'extra.label :=
- label 'last.label :=
- }
- if$
- number.label #1 + 'number.label :=
-}
-FUNCTION {reverse.pass}
-{ next.extra "b" =
- { "a" 'extra.label := }
- 'skip$
- if$
- extra.label 'next.extra :=
- extra.label
- emphasize
- duplicate$ empty$
- 'skip$
- { "{\natexlab{" swap$ * "}}" * }
- if$
- 'extra.label :=
- label extra.label * 'label :=
-}
-EXECUTE {initialize.extra.label.stuff}
-ITERATE {forward.pass}
-REVERSE {reverse.pass}
-FUNCTION {bib.sort.order}
-{ sort.label
- " "
- *
- year field.or.null sortify
- *
- " "
- *
- title field.or.null
- sort.format.title
- *
- #1 entry.max$ substring$
- 'sort.key$ :=
-}
-ITERATE {bib.sort.order}
-SORT
-FUNCTION {begin.bib}
-{ preamble$ empty$
- 'skip$
- { preamble$ write$ newline$ }
- if$
- "\begin{thebibliography}{" number.label int.to.str$ * "}" *
- write$ newline$
- "\expandafter\ifx\csname natexlab\endcsname\relax\def\natexlab#1{#1}\fi"
- write$ newline$
- "\expandafter\ifx\csname url\endcsname\relax"
- write$ newline$
- " \def\url#1{{\tt #1}}\fi"
- write$ newline$
- "\expandafter\ifx\csname urlprefix\endcsname\relax\def\urlprefix{URL }\fi"
- write$ newline$
-}
-EXECUTE {begin.bib}
-EXECUTE {init.state.consts}
-ITERATE {call.type$}
-FUNCTION {end.bib}
-{ newline$
- "\end{thebibliography}" write$ newline$
-}
-EXECUTE {end.bib}
-%% End of customized bst file
-%%
-%% End of file `ecology.bst'.
diff --git a/figures.R b/figures.R
index 1b9c0c5..ca5656d 100644
--- a/figures.R
+++ b/figures.R
@@ -386,3 +386,106 @@ points(structure,mns,cex=4,bg=cols,pch=21)
text(structure,(uplim+4),c('A','A'))
dev.off()
+
+#######################################
+
+# Generate maps
+
+current_dir <- getwd()
+
+suppressMessages(library(ggplot2))
+suppressMessages(library(sf))
+options(tidyverse.quiet=TRUE)
+library(tidyverse)
+suppressMessages(library(ggsn))
+
+#Get data
+setwd('~/research/gis/boundaries')
+mmyf_bounds = st_read('mmsf_ysf_boundaries.shp',quiet=T) %>%
+ mutate(is_forest = 'State Forest')
+hee_bounds = st_read('hee_cores.shp',quiet=T)[1:9,] %>%
+ mutate(Treatment = factor(Treatment, levels=c('Even-aged','Uneven-aged',
+ 'Control')))
+harvest_bounds = st_read('hee_harvests_2008.shp',quiet=T) %>%
+ mutate(HarvestTyp = factor(HarvestTyp,levels=c('clearcut','shelter',
+ 'patch','single-tree','no harvest')),
+ HarvestTyp = fct_recode(HarvestTyp,Clearcut='clearcut',
+ Shelterwood ='shelter',`Patch Cut` = 'patch',
+ `Single-tree` = 'single-tree',
+ `No Harvest` = 'no harvest'))
+
+bird_points = st_read('../experiments/hee_bird_points_all.shp',quiet=T) %>%
+ filter(Unit %in% 1:3) %>%
+ mutate(label = 'Bird Point')
+
+setwd(current_dir)
+
+#HEE map
+hee_coords = st_coordinates(hee_bounds)
+
+hee_map = mmyf_bounds %>% ggplot() +
+ geom_sf(aes(fill=is_forest)) +
+ geom_sf(data=hee_bounds,aes(fill=Treatment)) +
+ scale_fill_manual(name=NULL,
+ values=c('gray','firebrick1','gray95','dodgerblue'),
+ breaks=c('State Forest','Even-aged','Uneven-aged',
+ 'Control')) +
+ coord_sf(xlim=range(hee_coords[,'X']),
+ ylim=range(hee_coords[,'Y'])) +
+ theme_void() +
+ theme(axis.title.x=element_blank(),
+ axis.title.y=element_blank(),
+ axis.text.x=element_blank(),
+ axis.text.y=element_blank(),
+ legend.position=c(0.8,0.9),
+ legend.text=element_text(size=9),
+ legend.title=NULL,
+ panel.grid.major = element_line(color = 'transparent')) +
+ scalebar(data=hee_bounds,dist=2,dd2km=FALSE,st.size=3,location='bottomleft')
+
+ggsave('figures/hee_map.pdf')
+
+#Highlight subregion
+hee_sub = hee_bounds %>%
+ filter(UnitNumber %in% 1:3)
+
+subregion_box = st_as_sfc(st_bbox(st_buffer(hee_sub,500)))
+hee_map_sub = hee_map +
+ geom_sf(data=subregion_box,fill=NA,color='black',size=1.5) +
+ coord_sf(xlim=range(hee_coords[,'X']),
+ ylim=range(hee_coords[,'Y']))
+
+ggsave('figures/hee_map_sub.pdf')
+
+#Bird experiment map
+sub_coords = st_coordinates(hee_sub)
+
+sub_map = mmyf_bounds %>% ggplot() +
+ geom_sf(aes(fill=is_forest)) +
+ geom_sf(data=hee_sub) +
+ geom_sf(data=harvest_bounds,aes(fill=HarvestTyp)) +
+ geom_sf(data=bird_points,aes(color=label),show.legend='point') +
+ scale_color_manual(name=NULL, values=c('Bird Point' = 'black'),
+ guide = guide_legend(order=1)) +
+ scale_fill_manual(name=NULL,
+ values=c('firebrick1','gray','orange','dodgerblue',
+ 'forestgreen','gray95'),
+ breaks=c('State Forest','Clearcut','Shelterwood',
+ 'Patch Cut','Single-tree','No Harvest'),
+ guide = guide_legend(override.aes =
+ list(shape = NA),order=2,
+ title.position='bottom')) +
+ coord_sf(xlim=range(sub_coords[,'X']),
+ ylim=range(sub_coords[,'Y'])) +
+ theme_void() +
+ theme(axis.title.x=element_blank(),
+ axis.title.y=element_blank(),
+ axis.text.x=element_blank(),
+ axis.text.y=element_blank(),
+ legend.position=c(0.8,0.36),
+ legend.text=element_text(size=9),
+ legend.title=NULL,
+ panel.grid.major = element_line(color = 'transparent')) +
+ scalebar(hee_sub,dist=0.5,dd2km=F,st.size=3,location='topleft')
+
+ggsave('figures/hee_cores.pdf')
diff --git a/hee_map.R b/hee_map.R
deleted file mode 100644
index eb61651..0000000
--- a/hee_map.R
+++ /dev/null
@@ -1,85 +0,0 @@
-suppressMesssages(library(ggplot2))
-suppressMessages(library(sf))
-options(tidyverse.quiet=TRUE)
-library(tidyverse)
-suppressMessages(library(ggsn))
-
-setwd('~/research/gis/boundaries')
-
-mmyf_bounds = st_read('mmsf_ysf_boundaries.shp',quiet=T) %>%
- mutate(is_forest = 'State Forest')
-hee_bounds = st_read('hee_cores.shp',quiet=T)[1:9,] %>%
- mutate(Treatment = factor(Treatment, levels=c('Even-aged','Uneven-aged',
- 'Control')))
-harvest_bounds = st_read('hee_harvests_2008.shp',quiet=T) %>%
- mutate(HarvestTyp = factor(HarvestTyp,levels=c('clearcut','shelter',
- 'patch','single-tree','no harvest')),
- HarvestTyp = fct_recode(HarvestTyp,Clearcut='clearcut',
- Shelterwood ='shelter',`Patch Cut` = 'patch',
- `Single-tree` = 'single-tree',
- `No Harvest` = 'no harvest'))
-
-bird_points = st_read('../experiments/hee_bird_points_all.shp',quiet=T) %>%
- filter(Unit %in% 1:3) %>%
- mutate(label = 'Bird Point')
-
-hee_coords = st_coordinates(hee_bounds)
-
-hee_map = mmyf_bounds %>% ggplot() +
- geom_sf(aes(fill=is_forest)) +
- geom_sf(data=hee_bounds,aes(fill=Treatment)) +
- scale_fill_manual(name=NULL,
- values=c('gray','firebrick1','gray95','dodgerblue'),
- breaks=c('State Forest','Even-aged','Uneven-aged',
- 'Control')) +
- coord_sf(xlim=range(hee_coords[,'X']),
- ylim=range(hee_coords[,'Y'])) +
- theme_void() +
- theme(axis.title.x=element_blank(),
- axis.title.y=element_blank(),
- axis.text.x=element_blank(),
- axis.text.y=element_blank(),
- legend.position=c(0.8,0.9),
- legend.text=element_text(size=9),
- legend.title=NULL,
- panel.grid.major = element_line(color = 'transparent')) +
- scalebar(hee_bounds,dist=2,dd2km=F,st.size=3,location='bottomleft')
-
-hee_map
-
-##
-
-hee_sub = hee_bounds %>%
- filter(UnitNumber %in% 1:3)
-
-sub_coords = st_coordinates(hee_sub)
-
-sub_map = mmyf_bounds %>% ggplot() +
- geom_sf(aes(fill=is_forest)) +
- geom_sf(data=hee_sub) +
- geom_sf(data=harvest_bounds,aes(fill=HarvestTyp)) +
- geom_sf(data=bird_points,aes(color=label),show.legend='point') +
- scale_color_manual(name=NULL, values=c('Bird Point' = 'black'),
- guide = guide_legend(order=1)) +
- scale_fill_manual(name=NULL,
- values=c('firebrick1','gray','orange','dodgerblue',
- 'forestgreen','gray95'),
- breaks=c('State Forest','Clearcut','Shelterwood',
- 'Patch Cut','Single-tree','No Harvest'),
- guide = guide_legend(override.aes =
- list(shape = NA),order=2,
- title.position='bottom')) +
- coord_sf(xlim=range(sub_coords[,'X']),
- ylim=range(sub_coords[,'Y'])) +
- theme_void() +
- theme(axis.title.x=element_blank(),
- axis.title.y=element_blank(),
- axis.text.x=element_blank(),
- axis.text.y=element_blank(),
- legend.position=c(0.8,0.36),
- legend.text=element_text(size=9),
- legend.title=NULL,
- panel.grid.major = element_line(color = 'transparent')) +
- scalebar(hee_sub,dist=0.5,dd2km=F,st.size=3,location='topleft')
-
-sub_map
diff --git a/makefile b/makefile
index bda67cd..893c556 100644
--- a/makefile
+++ b/makefile
@@ -1,24 +1,17 @@
-BIBSTYLE = https://schneider.ncifcrf.gov/ftp/ecology.bst
-
-talk-fnr-2018.pdf: content.md talk.tex common.tex references.bib style.bst images figures
+talk-cu-2018.pdf: content.md talk.tex common.tex references.bib images figures
pandoc content.md --slide-level 2 --listings -t beamer -o content.tex
xelatex talk.tex
- bibtex talk
- xelatex talk.tex
+ biber talk
xelatex talk.tex
- pdftk talk.pdf cat 1-36 output talk1.pdf
- pdftk talk.pdf cat 37-end output talk2.pdf
+ pdfjam talk.pdf 1-36 --fitpaper true --outfile talk1.pdf
+ pdfjam talk.pdf 37- --fitpaper true --outfile talk2.pdf
gs -sDEVICE=pdfwrite -dMaxSubsetPct=100 -dPDFSETTINGS=/prepress -dEmbedAllFonts=true -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode -sOutputFile="talk1_small.pdf" -dNOPAUSE -dBATCH "talk1.pdf"
- pdftk talk1_small.pdf talk2.pdf cat output talk-fnr-2018.pdf
- rm talk.pdf talk1_small.pdf talk1.pdf talk2.pdf
- xdg-open talk-fnr-2018.pdf
+ pdfjam talk1_small.pdf talk2.pdf --fitpaper true --outfile talk-cu-2018.pdf
+ rm -f talk1_small.pdf talk2.pdf talk.pdf talk1.pdf
references.bib: content.md
pubs extract-tex content.md references.bib
-style.bst:
- wget -nc $(BIBSTYLE) -O style.bst
-
images: collect-images.sh image-sources.txt
@mkdir -p images
bash collect-images.sh
@@ -28,4 +21,4 @@ figures: figures.R data-sources.R
Rscript figures.R
clean:
- rm -fv *.aux *.log *.toc *.blg *.bbl *.synctex.gz *.out *.snm *.nav *.vrb content.tex *.bib
+ rm -fv *.aux *.log *.toc *.blg *.bbl *.synctex.gz *.out *.snm *.nav *.vrb content.tex *.bib *.run.xml *.bcf
diff --git a/talk.tex b/talk.tex
index d1a0218..ebc243d 100644
--- a/talk.tex
+++ b/talk.tex
@@ -39,8 +39,9 @@
\include{content}
\begin{frame}{References}
-\footnotesize
-\bibliography{references}
+\AtNextBibliography{\footnotesize}
+\setbeamertemplate{bibliography item}{}
+\printbibliography[heading=none]
\end{frame}
\end{document}